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User: Johannes Rainer

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Johannes Rainer1.4k
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Italy
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@jotsetung
Last seen:
2 days, 11 hours ago
Joined:
4 years, 3 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 262 results • page 1 of 27 • next >
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Comment: C: How to use EnsDb in annotatePeak from package "ChIPseeker"
... `intronsByTranscript` is exported in ensembldb version 2.6.6 which will be available in a few days. ...
written 2 days ago by Johannes Rainer1.4k
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Answer: A: How to use EnsDb in annotatePeak from package "ChIPseeker"
... The reason is that `ensembldb` doesn't have an `intronsByTranscript` method. I'll add that and it *should* work. cheers, jo ...
written 3 days ago by Johannes Rainer1.4k
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Answer: A: Retrieve canonical transcript for each gene via ensembldb R package
... At present I am not including this information to the ensembldb databases. So there is no way to get the canonical transcript for a gene using ensembldb. Sorry for that. ...
written 27 days ago by Johannes Rainer1.4k
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Comment: C: Troubles with mzR and BiocInstaller
... Also, the message is rather a warning than an error. mzR will most likely work as expected.   ...
written 8 weeks ago by Johannes Rainer1.4k
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Comment: C: make TxDb from list of genes
... I agree with James. No need to create a new TxDb database. You could simply subset an EnsDb database to your list of input genes (even better if you have Ensembl IDs): assuming you have your Ensembl gene IDs in a variable called ensids: library(EnsDb.Hsapiens.v86) edb <- filter(EnsDb.Hsapiens.v ...
written 10 weeks ago by Johannes Rainer1.4k
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Answer: A: Pick coding vs non-coding from Ensembl data set
... You can simply filter the complete EnsDb database to contain only protein coding genes or all other genes (note: this includes miRNA genes, lincRNAs, pseudogenes, snoRNA, scaRNA, sRNA, scRNA, rRNA ...). > library(EnsDb.Hsapiens.v86) > ## Filter the EnsDb database for protein coding genes > ...
written 11 weeks ago by Johannes Rainer1.4k
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Comment: C: Ensembl plants at annotationHub?
... I've generated the EnsDb. You can get the file from here https://www.dropbox.com/sh/wglt28zlfzhjubs/AADzGqJ0zydKRmdqbOsH_Ru5a?dl=0 after unzipping you can simply load the sqlite file with edb <- EnsDb(<sqlite-file>)   ...
written 12 weeks ago by Johannes Rainer1.4k
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Comment: C: Ensembl plants at annotationHub?
... Lori, do you think it might be usefull to add also EnsDb for all species in ensemblgenomes to AnnotationHub (starting ev "only" with plants)?   ...
written 12 weeks ago by Johannes Rainer1.4k
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Answer: A: Ensembl plants at annotationHub?
... Dear Guido, while it is possible to create EnsDb databases also for ensemblgenomes (including plants, funghi etc) I did not do this on a regular basis and was also hesitant to add these to AnnotationHub because I was not sure how many users there will be for these. Just let me know which species ( ...
written 3 months ago by Johannes Rainer1.4k
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Comment: C: R failing to load genome files from EnsDb.Hsapiens.v86
... Yes, looks like that. You could also specifically look in the package libary directory  (EnsDb.Hsapiens.v86/extdata) in the path where your library is (which you get with .libPaths() in R). Please let me know if re-installation solved the problem. ...
written 3 months ago by Johannes Rainer1.4k

Latest awards to Johannes Rainer

Scholar 3 months ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 3 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 3 months ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 3 months ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Popular Question 4 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 5 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 8 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 8 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Scholar 20 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 20 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 20 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 20 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 20 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 20 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 20 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 20 months ago, received more than 100 upvotes.
Voter 20 months ago, voted more than 100 times.
Scholar 20 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 20 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 21 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 21 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 22 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Scholar 22 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype

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